A genome catalog of the early-life human skin microbiome
Authors: Zeyang Shen, Lukian Robert, Milan Stolpman, You Che, Katrina J. Allen, Richard Saffery, Audrey Walsh, Angela Young, Jana Eckert, Clay Deming, Qiong Chen, Sean Conlan, Karen Laky, Jenny Min Li, Lindsay Chatman, Sara Saheb Kashaf, Beatrice B. Barnabas, Sean Black, Gerard G. Bouffard, Shelise Y. Brooks, Juyun Crawford, Holly Marfani, Lyudmila Dekhtyar, Joel Han, Shi-Ling Ho, Richelle Legaspi, Quino L. Maduro, Catherine A. Masiello, Jennifer C. McDowell, Casandra Montemayor, James C. Mullikin, Morgan Park, Nancy L. Riebow, Karen Schandler, Brian Schmidt, Christina Sison, Sirintorn Stantripop, James W. Thomas, Pamela J. Thomas, Meghana Vemulapalli, Alice C. Young, Kirsten Perrett, Justin Brown, Natalie Carvalho, Nigel Curtis, Kim Daziel, Shyamali Dharmage, Ronda Greaves, Lyle Gurrin, Li Huang, Jennifer Koplin, Katherine Lee, Georgia Paxton, Rachel Peters, Anne-Louise Ponsonby, Peter Sayre, Mimi Tang, Peter Vuillermin, Melissa Wake, Deborah Anderson, Christine Axelrad, Anna Bourke, Kirsty Bowes, Tim Brettig, Natasha Burgess, Beatriz Camesella-Perez, Xueyuan Che, Daniela Ciciulla, Jac Cushnahan, Helen Czech, Thanh Dang, Kathryn Dawes, Hannah Elborough, Michael Field, Charlie Fink, Sarah Fowler, Grace Gell, Rebecca Gray, Emi Habgood, Richard Hall, Phoebe Harris, Erin Hill, Kensuke Hoashi, Hannah Ilhan, Narelle Jenkins, Andrew Knox, Clare Morrison, Melanie Neeland, Jenn Ness, Wendy Norton, Sasha Odoi, Mary Panjari, Kayla Parker, Ahelee Rahman, Ashleigh Rak, Maisie Ralphsmith, Natalie Schreurs, Carrie Service, Victoria Soriano, Judith Spotswood, Mark Taranto, Leone Thiele, Kate Wall, Angela Walsh, Anita Wise, Andrew Davidson, Arul Earnest, Lara Ford, Andrew Kemp, Sam Mehr, Tibor Schuster, Dean Tey, Diana Zannino, Donna Legge, Jason Bell, Joanne Cheah, Kay Hynes, Kee Lim, Emily Porrello, Annette Powell, Pedro Ramos, Anushka Karunanayake, Izabelle Mezzetti, Kayla Parker, Ronita Singh, Harriet Edmund, Bridie Byrne, Tom Keeble, Cuby Martis, Belle Ngien, Penny Glenn, Andrew Kaynes, Heidi H. Kong, Pamela A. Frischmeyer-Guerrerio, Kirsten P. Perrett, Julia A. Segre
Journal: Genome biology (2023)

Abstract Background Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Results Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2–3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants. Conclusions Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.